Yep, that case is supposed to accept 120mm and 140mm fans up top so that shouldn't be an issue. I'm not sure why you think the motherboard would have any affect on this, but it should actually be beneficial to gaining space inside for RAM and GPU cards since there won't of course be a giant heatsink eating up all your real estate.
If you're not as concerned with aesthetics as you are with performance, you might even consider mounting the radiator outside the case on top and mounting the fans inside the case on top (Blowing out of course) to further free up the inside for cable management and cooling while also removing a significant portion of heat from inside the case by the fact of transplanting the radiator to a location where it won't be radiating any heat that escapes the fans, plus not blowing the hot air back inside the case as some installations require.
Just an idea that has worked well for some folks. But regardless of how you do it, it should be fine.